The chronic infections of cystic fibrosis (CF) airways with Pseudomonas aeruginosa are a paradigm of how environmental bacteria can conquer, adapt, and persist in an atypical habitat and successfully evade defense mechanisms and chemotherapy in a susceptible host. The within-host evolution of intraclonal diversity has been examined by whole-genome sequencing, phenotyping, and competitive fitness experiments of serial P. aeruginosa isolates collected from CF airways since onset of colonization for a period of up to 40 years. The spectrum of de novo mutations and the adaptation of phenotype and fitness of the bacterial progeny were more influenced by the living conditions in the CF lung than by the clone type of their ancestor and its genetic repertoire.

Pseudomonas aeruginosa (PA) is an opportunistic human pathogen, which is involved in a wide range of dangerous infections. It develops alarming resistances toward antibiotic treatment. Therefore, alternative strategies, which suppress pathogenicity or synergize with antibiotic treatments are in great need to combat these infections more effectively. One promising approach is to disarm the bacteria by interfering with their quorum sensing (QS) system, which regulates the release of various virulence factors as well as biofilm formation. Herein, this work reports the rational design, optimization, and in-depth profiling of a new class of Pseudomonas quinolone signaling receptor (PqsR) inverse agonists. The resulting frontrunner compound features a pyrimidine-based scaffold, high in vitro and in vivo efficacy, favorable pharmacokinetics as well as clean safety pharmacology characteristics, which provide the basis for potential pulmonary as well as systemic routes of administration. An X-ray crystal structure in complex with PqsR facilitated further structure-guided lead optimization. The compound demonstrates potent pyocyanin suppression, synergizes with aminoglycoside antibiotic tobramycin against PA biofilms, and is active against a panel of clinical isolates from bronchiectasis patients. Importantly, this in vitro effect translated into in vivo efficacy in a neutropenic thigh infection model in mice providing a proof-of-principle for adjunctive treatment scenarios.

Chronic airway infections with Pseudomonas aeruginosa are the major co-morbidity in most people with cystic fibrosis (CF) sustained by neutrophils as the major drivers of lung inflammation, damage, and remodeling. Phagocytosis assays were performed with clonal consortia of longitudinal P. aeruginosa airway isolates collected from people with CF since the onset of lung colonization until patient's death or replacement by another clone. The extra-and intra-cellular abundance of individual strains was assessed by deep amplicon sequencing of strain-specific single nucleotide variants in the bacterial genome. The varied microevolution of the accessory genome of the P. aeruginosa clones during mild and severe courses of infection corresponded with a differential persistence of clonal progeny in the neutrophil phagosome. By simultaneously exposing the ancestor and its progeny to the same habitat, the study recapitulated the time lapse of the temporal change of the fitness of the clone to survive in neutrophils.

Drug-resistant Pseudomonas aeruginosa (PA) poses an emerging threat to human health with urgent need for alternative therapeutic approaches. Here, we deciphered the B cell and antibody response to the virulence-associated type III secretion system (T3SS) in a cohort of patients chronically infected with PA. Single-cell analytics revealed a diverse B cell receptor repertoire directed against the T3SS needle-tip protein PcrV, enabling the production of monoclonal antibodies (mAbs) abrogating T3SS-mediated cytotoxicity. Mechanistic studies involving cryoelectron microscopy identified a surface-exposed C-terminal PcrV epitope as the target of highly neutralizing mAbs with broad activity against drug-resistant PA isolates. These anti-PcrV mAbs were as effective as treatment with conventional antibiotics in vivo. Our study reveals that chronically infected patients represent a source of neutralizing antibodies, which can be exploited as therapeutics against PA.

Genome sequencing of 130 Pseudomonas aeruginosa isolates from 110 bronchiectasis patients identified a few dominant clones common in the global bacterial population and numerous rare clones infrequently seen in the environment or other human infections https://bit.ly/3lIfD2X.

Chronic respiratory infections with the gram-negative bacterium Pseudomonas aeruginosa are an important co-morbidity for the quality of life and prognosis of people with cystic fibrosis (CF). Such long-term colonization, sometimes lasting up to several decades, represents a unique opportunity to investigate pathogen adaptation processes to the host. Our studies aimed to resolve if and to what extent the bacterial adaptation to the CF airways influences the fitness of the pathogen to grow and to persist in the lungs. Marker-free competitive fitness experiments of serial P. aeruginosa isolates differentiated by strain-specific SNPs, were performed with murine and human precision cut lung slices (PCLS). Serial P. aeruginosa isolates were selected from six mild and six severe CF patient courses, respectively. MPCLS or hPCLS were inoculated with a mixture of equal numbers of the serial isolates of one course. The temporal change of the composition of the bacterial community during competitive growth was quantified by multi-marker amplicon sequencing. Both ex vivo models displayed a strong separation of fitness traits between mild and severe courses. Whereas the earlier isolates dominated the competition in the severe courses, intermediate and late isolates commonly won the competition in the mild courses. The status of the CF lung disease rather than the bacterial genotype drives the adaptation of P. aeruginosa during chronic CF lung infection. This implies that the disease status of the lung habitat governed the adaptation of P. aeruginosa more strongly than the underlying bacterial clone-type and its genetic repertoire.

The metabolically versatile Pseudomonas aeruginosa inhabits biotic and abiotic environments including the niche of cystic fibrosis (CF) airways. This study investigated how the adaptation to CF lungs affects the within-clone fitness of P. aeruginosa to grow and persist in liquid cultures in the presence of the clonal ancestors. Longitudinal clonal P. aeruginosa isolates that had been collected from 12 CF donors since the onset of colonization for up to 30 years was subjected to within-clone competition experiments. The relative quantities of individual strains were determined by marker-free amplicon sequencing of multiplex PCR products of strain-specific nucleotide sequence variants, a novel method that is generally applicable to studies in evolutionary genetics and microbial ecology with real-world strain collections. For 10 of the 12 examined patient courses, P. aeruginosa isolates of the first years of colonization grew faster in the presence of their clonal progeny than alone. Single growth of individual strains showed no temporal trend with colonization time, but in co-culture, the early isolates out-competed their clonal progeny. Irrespective of the genetic make-up of the clone and its genomic microevolution in CF lungs, the early isolates expressed fitness traits to win the within-clone competition that were absent in their progeny.

The nosocomial acquisition of opportunistic pathogens, particularly Pseudomonas aeruginosa , has been repeatedly documented in individuals with cystic fibrosis (CF) [1]. Cross-infection is also a concern in bronchiectasis not due to CF [2]. This issue was not addressed by the European Respiratory Society 2017 guidelines for the management of adult bronchiectasis [3] but the European Bronchiectasis Network (EMBARC), the EMBARC Patient Advisory Group and the European Reference Network (ERN-Lung) Bronchiectasis Network released a position statement in the European Respiratory Journal in 2018 [4]. Based on the available evidence, the risk of cross-infection with P. aeruginosa was judged to be small. This study suggests that the risk of cross-infection with P. aeruginosa in bronchiectasis is small

Chronic airway infections with Pseudomonas aeruginosa determine morbidity in most individuals with cystic fibrosis (CF). P. aeruginosa may persist for decades in CF lungs, which provides a rare opportunity to study the long-term within-host evolution of a bacterial airway pathogen. In this work, we sought to resolve the genetic adaptation of P. aeruginosa in CF lungs from the onset of colonization until the patient's death or permanent replacement by another P. aeruginosa clone. We followed the microevolution of the first persisting P. aeruginosa clone by whole-genome sequencing of serial isolates from highly divergent clinical courses of airway infection, i.e., a fatal outcome because of respiratory insufficiency within less than 15 years, or a rather normal daily life 25-35 years after acquisition of P. aeruginosa. Nonneutral mutations predominantly emerged in P. aeruginosa genes relevant for protection against and communication with signals from the lung environment, i.e., antibiotic resistance, cell wall components, and two-component systems. Drastic and loss-of-function mutations preferentially happened during the severe courses of infection, and the bacterial lineages of the mild courses more proficiently incorporated extra metabolic genes into their accessory genome. P. aeruginosa followed different evolutionary paths depending on whether the bacterium had taken up residence in a patient with CF and normal or already compromised lung function.

Background: Early antimicrobial chemotherapy can prevent or at least delay chronic cystic fibrosis (CF) airways infections with Pseudomonas aeruginosa.Methods: During a 10-year study period P. aeruginosa was detected for the first time in 54 CF patients regularly seen at the CF centre Hannover. Amplicon sequencing of 34 loci of the P. aeruginosa core genome was performed in baseline and post-treatment isolates of the 15 CF patients who had remained P. aeruginosa positive after the first round of antipseudomonal chemotherapy.Results: Deep sequencing uncovered coexisting alternative nucleotides at in total 33 of 55,284 examined genome positions including six non synonymous polymorphisms in the lasR gene, a key regulator of quorum sensing. After early treatment 42 of 50 novel nucleotide substitutions had emerged in exopolysaccharide biosynthesis, efflux pump and porin genes.Conclusions: Early treatment selects pathoadaptive mutations in P. aeruginosa that are typical for chronic infections of CF lungs. (C) 2016 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Cystic fibrosis (CF) is the most frequent congenital lethal disease in Caucasians. Impaired mucociliary clearance causes chronic bacterial rhinosinusitis in up to 62% of patients, and almost all patients exhibit sinonasal pathology in CT scans. Pathogens like Pseudomonas aeruginosa (P.a.) chronically colonize about 70% of the CF adults’ lungs and are the major reason for pulmonary destruction and premature death. In our 34-year-old female CF patient, rhinosinusitis caused massive orbital hypertelorism despite three sinonasal operations. Her sputum samples had always been negative for P.a. Then, P.a. was primarily detected in her sputum and additionally in nasal lavage, which since then persisted in both, her upper and lower airways. The P.a. strains turned out to be genetically identical in both airway levels, indicating early colonization of the entire airway system with P.a. This first report on simultaneous primary P.a. detection in the sinonasal and pulmonary compartments highlights the need to include an assessment of upper airway colonization in the standards of CF care, particularly in patients without chronic P.a. colonization. Both airway levels need to be considered as one united system, and a strong cooperation between ENT and CF specialists should be established. Prospective longitudinal studies should assess the upper airways´ role in acquisition and persistence of pathogens and evaluate conservative and surgical therapeutic options.

SummaryBacterial populations differentiate at the subspecies level into clonal complexes. Intraclonal genome diversity was studied in 100 isolates of the two dominant Pseudomonas aeruginosa clones C and PA14 collected from the inanimate environment, acute and chronic infections. The core genome was highly conserved among clone members with a median pairwise within‐clone single nucleotide sequence diversity of 8 × 10−6 for clone C and 2 × 10−5 for clone PA14. The composition of the accessory genome was, on the other hand, as variable within the clone as between unrelated clones. Each strain carried a large cargo of unique genes. The two dominant worldwide distributed P. aeruginosa clones combine an almost invariant core with the flexible gain and loss of genetic elements that spread by horizontal transfer.

ABSTRACT The chronic airway infections with Pseudomonas aeruginosa in people with cystic fibrosis (CF) are treated with aerosolized antibiotics, oral fluoroquinolones, and/or intravenous combination therapy with aminoglycosides and β-lactam antibiotics. An international strain collection of 361 P. aeruginosa isolates from 258 CF patients seen at 30 CF clinics was examined for mutations in 17 antimicrobial susceptibility and resistance loci that had been identified as hot spots of mutation by genome sequencing of serial isolates from a single CF clinic. Combinatorial amplicon sequencing of pooled PCR products identified 1,112 sequence variants that were not present in the genomes of representative strains of the 20 most common clones of the global P. aeruginosa population. A high frequency of singular coding variants was seen in spuE , mexA , gyrA , rpoB , fusA1 , mexZ , mexY , oprD , ampD , parR , parS , and envZ ( amgS ), reflecting the pressure upon P. aeruginosa in lungs of CF patients to generate novel protein variants. The proportion of nonneutral amino acid exchanges was high. Of the 17 loci, mexA , mexZ , and pagL were most frequently affected by independent stop mutations. Private and de novo mutations seem to play a pivotal role in the response of P. aeruginosa populations to the antimicrobial load and the individual CF host.

The population genomics of Pseudomonas aeruginosa was analysed by genome sequencing of representative strains of the 15 most frequent clonal complexes in the P. aeruginosa population and of the five most common clones from the environment of which so far no isolate from a human infection has been detected. Gene annotation identified 5892-7187 open reading frame (ORFs; median 6381 ORFs) in the 20 6.4-7.4 Mbp large genomes. The P. aeruginosa pangenome consists of a conserved core of at least 4000 genes, a combinatorial accessory genome of a further 10 000 genes and 30 000 or more rare genes that are present in only a few strains or clonal complexes. Whole genome comparisons of single nucleotide polymorphism synteny indicated unrestricted gene flow between clonal complexes by recombination. Using standardized acute lettuce, Galleria mellonella and murine airway infection models the full spectrum of possible host responses to P. aeruginosa was observed with the 20 strains ranging from unimpaired health following infection to 100% lethality. Genome comparisons indicate that the differential genetic repertoire of clones maintains a habitat-independent gradient of virulence in the P. aeruginosa population.

High-throughput genome sequencing of serial isolates from cystic fibrosis (CF) airways collected over a 30-year period uncovered targets of antipseudomonal chemotherapy as hot-spots of mutation. Sporadic mutations were overrepresented in the loci gyrA, rpoB, ampD, mexA, mexS, mexY, mexZ, parS, parR, amrZ, envZ, oprD, oprM, pagL, spuE, spuF, fusA1 and fusA2. To reveal the frequency and spectrum of single nucleotide variations and frame-shift mutations in these loci in the contemporary P. aeruginosa population residing in CF airways, deep amplicon sequencing was performed with loci-spanning 405–1554 bp large PCR products amplified from DNA pooled from two strain collections. 305 isolates were obtained from 209 CF patients seen at 51 CF centers in Europe and USA and 56 isolates were retrieved from 38 CF patients after they had received early antipseudomonal chemotherapy of first lower airways colonization with P. aeruginosa. The impact of missense, stop and frame-shift mutations on bacterial antimicrobial susceptibility phenotype was assessed by determination of MIC values against amikacin, aztreonam, cefepime, ceftazidime, ciprofloxacin, colistin, doripenem, fosfomycin, ghentamycin, imipenem, levofloxacin, meropenem, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam and tobramycin. The spectrum of SNPs and indels and their association in the 18 susceptibility loci with the antipseudomonal resistance phenotype will be presented at the meeting. Supported by DFG (SFB 900, A2) and BMBF (DZL at BREATH).

SummaryThe population structure of the cosmopolitan Pseudomonas aeruginosa was investigated by genotyping 2921 isolates from 1448 independent habitats with a custom‐made 58 binary marker microarray. Of 323 identified clone types, 109 clones made up 82% of the population. The 20 most frequent clones had an absolute share of 44% indicating that the P. aeruginosa population is dominated by few epidemic clonal complexes. The frequency distribution of common clones was different between inanimate habitats and human niches. The three most abundant clones in the environment were rare among isolates from human infection. Conversely, disease‐associated isolates either belonged to ubiquitous clones such as C and PA14 or to clones that were uncommon in the environment. The P. aeruginosa population consists of major clones that are just as versatile in their habitat and geographic origin as the whole species and of minor clones with preference for a peculiar niche.

Objective: Burkholderia cenocepacia (Bc) is a highly antimicrobially resistant pathogen, which is rarely eradicated from cystic fibrosis (CF) patients.While Bc is generally confined to the lung, bacteraemia can develop in a subgroup of patients contributing to a sharp decline in health.How Bc chronically colonises and causes bacteraemia remain poorly understood.Bacteria can change phenotype during infection, adapting to the host environment.We aim to identify the alterations in Bc phenotype from initial colonisation to chronic infection.Methods: A series of genetically identical sequential Bc isolates from two siblings with CF, one with chronic infection confined to the lung (Pt1), the other with bacteraemia (Pt2), were studied.In vivo virulence using Galleria mellonella, mucoidy on yeast extract mannitol (YEM) agar and adhesion to CF lung epithelial cells (CFBE41o-) were examined.Results: All isolates were relatively avirulent in vivo in Galleria mellonella.The blood isolates from Pt2 were considerably more virulent than a sputum isolate from that patient (P = 0.014).Mucoid production by Bc has been associated with better patient outcomes; however, all but one isolate were non-mucoid on YEM.Both sputum and blood isolates increased attachment to CFBEs over time of colonisation (p < 0.005 and 0.001 respectively), indicating an increased potential for host epithelial interactions over time.This key adaptation was confirmed by confocal microscopy.We are currently comparing the proteomes of all isolates to identify alterations in protein expression that may be involved.